From 59eee452c70476a747d63e188f6d1359cfaf6aff Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Oct 2026 20:27:45 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: v2.3.10 → v2.5.15](https://github.com/biomejs/pre-commit/compare/v2.3.10...v2.5.15)
- [github.com/tox-dev/pyproject-fmt: v2.11.1 → v2.30.3](https://github.com/tox-dev/pyproject-fmt/compare/v2.11.1...v2.30.3)
- [github.com/astral-sh/ruff-pre-commit: v0.14.14 → v0.17.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.14...v0.17.1)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f3021c8..ad5aaf6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.10
+    rev: v2.5.15
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.11.1
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.17.1
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

From ad643e3b5f96e08d699a31240db0508808b5ea71 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Oct 2026 20:29:00 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a9bb2c8..fbc298d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,6 +20,7 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
+  "Programming Language :: Python :: 3.15",
 ]
 dependencies = [
   "anndata>=0.12",
@@ -100,9 +101,7 @@ doc = [
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -136,19 +135,19 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
-testpaths = [ "tests" ]
-xfail_strict = true
-addopts = [
+[tool.pytest]
+ini_options.testpaths = [ "tests" ]
+ini_options.addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
+ini_options.xfail_strict = true
 
-[tool.coverage.run]
-source = [ "multigrate" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.source = [ "multigrate" ]
+run.omit = [
   "**/test_*.py",
 ]
+run.patch = [ "subprocess" ]
 
 [tool.cruft]
 skip = [